Tumorigenic activation around HPV integrated sites in head and neck squamous cell carcinoma

Abstract

Human papillomavirus (HPV) is causally involved in the development of head and neck squamous cell carcinoma (HNSCC). The integration of HPV drives tumorigenesis through expression of oncogenic viral genes as well as genomic alterations in surrounding regions. To elucidate involvement of epigenetic dysregulation in tumorigenesis, we here performed integrated analyses of the epigenome, transcriptome and interactome using ChIP‐seq, RNA‐seq and Hi‐C and 4C‐seq for HPV(+) HNSCCs. We analyzed clinical HNSCC using The Cancer Genome Atlas data and found that genes neighboring HPV integration sites were significantly upregulated and were correlated with oncogenic phenotypes in HPV(+) HNSCCs. While we found four HPV integration sites in HPV(+) HNSCC cell line UPCI‐SCC‐090 through target enrichment sequencing, 4C‐seq revealed 0.5 to 40 Mb of HPV‐interacting regions (HPVIRs) where host genomic regions interacted with integrated HPV genomes. While 9% of the HPVIRs were amplified and activated epigenetically forming super‐enhancers, the remaining non‐amplified regions were found to show a significant increase in H3K27ac levels and an upregulation of genes associated with GO terms, for example, Signaling by WNT and Cell Cycle. Among those genes, ITPR3 was significantly upregulated, involving UPCI‐SCC‐090‐specific super‐enhancer formation around the ITPR3 promoter and in the 80‐kb‐downstream region. The knockdown of ITPR3 by siRNA or CRISPR deletions of the distant enhancer region led to a significant suppression of cell proliferation. The epigenetic activation of HPVIRs was also confirmed in other cell lines, UM‐SCC‐47 and UM‐SCC‐104. These data indicate that epigenetic activation in HPVIRs contributes, at least partially, to genesis of HPV(+) HNSCC.

Genomic structures and regulation patterns at HPV integration sites in cervical cancer

“…HPV integration can lead to changes in the sequence content of HPV, viral gene copy number, and epigenetic regulation of the viral genome [5][6][7][8] . Genomic and epigenomic changes can also occur in adjacent human genomic regions [9][10][11][12] , and may have cancer-promoting consequences, as they often include oncogenes within or near the site of HPV integration 13 .…”

Human papilloma virus hijacks enhancers to activate oncogenes in head and neck squamous cell carcinoma cells

“…To address that issue, Mima et al performed an integrative epigenomic and transcriptomic analysis in HPV-positive HNSCCs. 8 They first performed Hi-C (high-throughput chromosome conformation capture) analysis, which enabled them to assess global chromatin interaction across the genome and obtain an overview of the open (active) and closed (inactive) chromatin regions (termed A and B compartments) within the genome of nasopharyngeal epithelial cells. Through comparison with known HPV integration sites (breakpoints) in clinical HNSCCs in The Cancer Genome Atlas datasets, they found that a majority of the breakpoints were located within active chromatin regions.…”

“…Using 4C-seq analysis with an HPV-positive HNSCC cell line, Mima et al also identified regions where integrated HPVs and the host genome functionally interact (termed as HPV-interacting regions, HPVIRs). 8 Among the approximately 800 genes within the HPVIRs, the majority were located within active regions and their expression was increased regardless of their genomic amplification status. In fact, the largest number of genes within HPVIRs were located within active but nonamplified regions and were associated with WNT signaling and the cell cycle, which is suggestive of their functional importance to tumorigenesis.…”

“…To address that issue, Mima et al performed an integrative epigenomic and transcriptomic analysis in HPV‐positive HNSCCs 8 . They first performed Hi‐C (high‐throughput chromosome conformation capture) analysis, which enabled them to assess global chromatin interaction across the genome and obtain an overview of the open (active) and closed (inactive) chromatin regions (termed A and B compartments) within the genome of nasopharyngeal epithelial cells.…”

“…Using 4C‐seq analysis with an HPV‐positive HNSCC cell line, Mima et al also identified regions where integrated HPVs and the host genome functionally interact (termed as HPV‐interacting regions, HPVIRs) 8 . Among the approximately 800 genes within the HPVIRs, the majority were located within active regions and their expression was increased regardless of their genomic amplification status.…”